def constructor(self):
self.input("mystring", Optional[str], value="")
self.input("mystring_backup", Optional[str])
self.step(
"print",
EchoTestTool(inp=If(IsDefined(self.mystring), self.mystring,
self.mystring_backup)),
)
self.output("out", source=self.print)
def test_array_step_input(self):
wf = WorkflowBuilder("cwl_test_array_step_input")
wf.input("inp1", Optional[str])
wf.input("inp2", Optional[str])
wf.step(
"print",
ArrayTestTool(
inps=[
If(IsDefined(wf.inp1), wf.inp1, "default1"),
If(IsDefined(wf.inp2), wf.inp2 + "_suffix", ""),
]
),
),
wf.output("out", source=wf.print)
ret, _, _ = wf.translate("cwl", allow_empty_container=True, to_console=False)
self.maxDiff = None
self.assertEqual(cwl_arraystepinput, ret)
def arguments(self):
return [
ToolArgument(
StringFormatter(
"-Xmx{memory}G {compression} {otherargs}",
memory=MemorySelector() * 3 / 4,
compression=If(
IsDefined(InputSelector("compression_level")),
"-Dsamjdk.compress_level=" +
InputSelector("compression_level"),
"",
),
otherargs=JoinOperator(
FirstOperator([InputSelector("javaOptions"), []]),
" "),
),
prefix="--java-options",
position=-1,
)
]
def test_basic(self):
w = WorkflowBuilder("my_conditional_workflow")
w.input("inp", String(optional=True))
w.step(
"print_if_has_value",
TestTool(testtool=w.inp),
# only print if the input "inp" is defined.
when=IsDefined(w.inp),
)
w.output("out", source=w.print_if_has_value)
inputs_dict = {"inp": ToolInput("inp", str)}
c = cwl.translate_step_node(w.print_if_has_value, inputs_dict=inputs_dict)[0]
self.assertEqual("$((inputs.__when_inp != null))", c.when)
extra_input: cwlgen.WorkflowStepInput = c.in_[-1]
self.assertEqual("__when_inp", extra_input.id)
def arguments(self):
return [
# CADD
ToolArgument(
If(
IsDefined(InputSelector("caddReference")),
"--plugin CADD,"
+ JoinOperator(
InputSelector("caddReference").assert_not_null(), ","
),
"",
),
shell_quote=False,
),
# Condel
ToolArgument(
If(
IsDefined(InputSelector("condelConfig")),
"--plugin "
+ StringFormatter(
"Condel,{condelconfig},b",
condelconfig=InputSelector("condelConfig").assert_not_null(),
),
"",
),
shell_quote=False,
),
# dbNSFP
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("dbnspReference")),
IsDefined(InputSelector("dbsnpColumns")),
),
"--plugin "
+ StringFormatter(
"dbNSFP,{ref},{cols}",
ref=InputSelector("dbnspReference").assert_not_null(),
cols=JoinOperator(
InputSelector("dbsnpColumns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
# REVEL
ToolArgument(
If(
IsDefined(InputSelector("revelReference")),
"--plugin "
+ StringFormatter(
"REVEL,{ref}",
ref=InputSelector("revelReference").assert_not_null(),
),
"",
),
shell_quote=False,
),
# CUSTOM 1
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("custom1Reference")),
IsDefined(InputSelector("custom1Columns")),
),
"--custom "
+ StringFormatter(
"{ref},{cols}",
ref=InputSelector("custom1Reference").assert_not_null(),
cols=JoinOperator(
InputSelector("custom1Columns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
# CUSTOM 2
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("custom2Reference")),
IsDefined(InputSelector("custom2Columns")),
),
"--custom "
+ StringFormatter(
"{ref},{cols}",
ref=InputSelector("custom2Reference").assert_not_null(),
cols=JoinOperator(
InputSelector("custom2Columns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
]
def is_not_null(self):
from janis_core.operators.logical import IsDefined
return IsDefined(self)